SUMMARY Understanding the cellular and molecular processes underlying granulocyte homeostasis is crucial because producing too few granulocytes results in increased risk for infection (neutropenia), while producing too many granulocytes can result in severe tissue damage and death (myeloproliferative disorders). To delineate the molecular mechanisms underlying homeostatic neutrophil production, we previously delineated hierarchical genomic and regulatory states culminating in neutrophil or macrophage specification. Myeloid cells undergoing lineage specification traverse successive states of mixed-lineage gene expression dictated by antagonistic transcriptional programs (HSCP vs. myeloid progenitor, then Irf8 vs. Gfi1) that culminate in generation of neutrophil or monocyte precursors. Using neutropenia-patient-derived mutations in the GFI1 transcription factor, we generated mouse models of congenital neutropenia. To delineate the molecular mechanisms underlying homeostatic neutropenia and innate immune dysfunction in these mice, we first captured normal cell states encompassing neutrophil specification and commitment, then built a computational approach to assign neutropenia-model cells to normal cell states and assess cell-state specific variation in gene expression. Surprisingly, the majority of differentially expressed GFI1-target genes are sequentially altered as cells traverse successive states. Underscoring these cell state-specific insights, genetic rescue impacts specification but not innate immunity programmed during commitment. Here, we propose to provide regulatory insight explaining this finding; defining altered Gfi1-mutant binding and stage-specific open chromatin. Next, we will determine how neutrophil defense functions are programmed during commitment, and how that fails in humans and mice with neutropenia. Finally, we will revisit the gene regulatory network underlying homeostatic neutrophil versus macrophage specification in the context of establishing neutrophil homeostasis through waves of neonatal gut microbiome colonization. We propose that mouse modeling of mutations identified in neutropenic patients can be exploited to reveal the essential pathobiology of neutropenia, and to dissect mechanisms underlying normal innate immune function and the establishment of granulocyte homeostasis. 1